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- PDB-5gor: Crystal structure of alkaline invertase InvA from Anabaena sp. PC... -

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Basic information

Entry
Database: PDB / ID: 5gor
TitleCrystal structure of alkaline invertase InvA from Anabaena sp. PCC 7120
ComponentsAlkaline Invertase
KeywordsHYDROLASE / alkaline invertases / cyanobacteria / glycoside hydrolase family 100 / sucrose hydrolysis
Function / homologyGlycosyl hydrolase family 100 / Alkaline and neutral invertase / endo-alpha-N-acetylgalactosaminidase activity / beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / beta-fructofuranosidase
Function and homology information
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.673 Å
AuthorsXie, J. / Cai, K. / Hu, H.X. / Jiang, Y.L. / Yang, F. / Hu, P.F. / Chen, Y. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370757 China
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural Analysis of the Catalytic Mechanism and Substrate Specificity of Anabaena Alkaline Invertase InvA Reveals a Novel Glucosidase
Authors: Xie, J. / Cai, K. / Hu, H.X. / Jiang, Y.L. / Yang, F. / Hu, P.F. / Cao, D.D. / Li, W.F. / Chen, Y. / Zhou, C.Z.
History
DepositionJul 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline Invertase
B: Alkaline Invertase
C: Alkaline Invertase
D: Alkaline Invertase
E: Alkaline Invertase
F: Alkaline Invertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,99313
Polymers325,3456
Non-polymers6497
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28530 Å2
ΔGint-220 kcal/mol
Surface area85580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.171, 179.282, 96.362
Angle α, β, γ (deg.)90.00, 105.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alkaline Invertase / Alr1521 protein


Mass: 54224.141 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / Gene: invA, alr1521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YWS9, beta-fructofuranosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 27% PEG 6k, 0.1 M Becine

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: SAGITALLY FOCUSED Si(111)
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2015
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 84349 / % possible obs: 95.4 % / Redundancy: 2.9 % / Net I/σ(I): 10.8
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.1 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GOO

5goo


Resolution: 2.673→30.497 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 4215 5 %RANDOM
Rwork0.1918 ---
obs0.194 84298 95.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.673→30.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21982 0 41 252 22275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122642
X-RAY DIFFRACTIONf_angle_d0.97630711
X-RAY DIFFRACTIONf_dihedral_angle_d13.3168261
X-RAY DIFFRACTIONf_chiral_restr0.0433220
X-RAY DIFFRACTIONf_plane_restr0.0053960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6726-2.7030.37461290.25562548X-RAY DIFFRACTION93
2.703-2.73470.32031650.25752672X-RAY DIFFRACTION97
2.7347-2.76810.31671450.25792696X-RAY DIFFRACTION97
2.7681-2.80310.35321580.24452707X-RAY DIFFRACTION98
2.8031-2.83990.29631350.24632741X-RAY DIFFRACTION96
2.8399-2.87880.28541420.23412678X-RAY DIFFRACTION98
2.8788-2.91990.30331240.23482731X-RAY DIFFRACTION96
2.9199-2.96350.31611320.23332716X-RAY DIFFRACTION97
2.9635-3.00970.27841370.22942708X-RAY DIFFRACTION96
3.0097-3.0590.34881290.22142693X-RAY DIFFRACTION97
3.059-3.11170.26541410.22382688X-RAY DIFFRACTION96
3.1117-3.16830.25521300.22682715X-RAY DIFFRACTION97
3.1683-3.22910.30351550.22442700X-RAY DIFFRACTION96
3.2291-3.2950.27371460.23872670X-RAY DIFFRACTION97
3.295-3.36650.28271560.22582650X-RAY DIFFRACTION96
3.3665-3.44470.24711350.22142723X-RAY DIFFRACTION95
3.4447-3.53080.27011460.20442683X-RAY DIFFRACTION97
3.5308-3.62610.22121330.19672690X-RAY DIFFRACTION96
3.6261-3.73260.24511350.19282662X-RAY DIFFRACTION95
3.7326-3.85280.24771430.18912699X-RAY DIFFRACTION95
3.8528-3.99030.19891600.18122655X-RAY DIFFRACTION96
3.9903-4.14970.22461330.17642682X-RAY DIFFRACTION95
4.1497-4.3380.23871390.16562627X-RAY DIFFRACTION95
4.338-4.5660.24221340.17012675X-RAY DIFFRACTION94
4.566-4.8510.20321320.15922659X-RAY DIFFRACTION94
4.851-5.22390.20921480.17022609X-RAY DIFFRACTION94
5.2239-5.74640.21591310.18142553X-RAY DIFFRACTION91
5.7464-6.57070.1961540.18322638X-RAY DIFFRACTION94
6.5707-8.25110.15771360.16792641X-RAY DIFFRACTION93
8.2511-30.49890.17411320.1562574X-RAY DIFFRACTION90

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